Investigation of intra-hospital SARS-CoV-2 transmission using nanopore whole-genome sequencing

Løvestad, Alexander Hesselberg; Jørgensen, Silje Bakken; Handal, Nina; Ambur, Ole Herman; Aamot, Hege Vangstein

doi:10.1016/j.jhin.2021.02.022

Cited by 30 publications

(36 citation statements)

References 35 publications

(31 reference statements)

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“…To overcome these short-read sequencing issues, there are two technologies carrying promise for studies of viral genome instability by generating long reads from individual polynucleotides, Oxford Nanopore Technology and Pacific Biosciences [ 147 ]. Each of the two platforms is plagued by a rather high sequencing error rate, but even with the current level of accuracy Oxford Nanopore was used for characterizing viromes [ 148 , 149 , 150 ]. Any further increase in sequencing accuracy may cause a revolution with viral genome instability research.…”

Section: Concluding Remarks and Future Questionsmentioning

confidence: 99%

From RNA World to SARS-CoV-2: The Edited Story of RNA Viral Evolution

Kockler

Gordenin

2021

Cells

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The current SARS-CoV-2 pandemic underscores the importance of understanding the evolution of RNA genomes. While RNA is subject to the formation of similar lesions as DNA, the evolutionary and physiological impacts RNA lesions have on viral genomes are yet to be characterized. Lesions that may drive the evolution of RNA genomes can induce breaks that are repaired by recombination or can cause base substitution mutagenesis, also known as base editing. Over the past decade or so, base editing mutagenesis of DNA genomes has been subject to many studies, revealing that exposure of ssDNA is subject to hypermutation that is involved in the etiology of cancer. However, base editing of RNA genomes has not been studied to the same extent. Recently hypermutation of single-stranded RNA viral genomes have also been documented though its role in evolution and population dynamics. Here, we will summarize the current knowledge of key mechanisms and causes of RNA genome instability covering areas from the RNA world theory to the SARS-CoV-2 pandemic of today. We will also highlight the key questions that remain as it pertains to RNA genome instability, mutations accumulation, and experimental strategies for addressing these questions.

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Section: Concluding Remarks and Future Questionsmentioning

confidence: 99%

From RNA World to SARS-CoV-2: The Edited Story of RNA Viral Evolution

Kockler

Gordenin

2021

Cells

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“…Novel single nucleotide polymorphism (SNP) (also known as sample-unique variants) was defined as specific nucleotide substitution in viral genome present in the corresponding sample only. A similar approach has been used to determine intra-hospital transmission of SARS-CoV-2 [ 2 , 5 ]. Multiple sequence alignment for consensus genomes was performed by Clustal Omega 1.2.0 ( http://www.clustal.org/omega/ ).…”

Section: Methodsmentioning

confidence: 99%

“…The current wave of community outbreak of coronavirus disease 2019 (COVID-19) in Hong Kong at the time of writing commenced in November 2020 and the total number of symptomatic and asymptomatic infected cases was greater than in previous waves. When there are ongoing outbreaks of COVID-19, healthcare workers (HCWs) may acquire the disease from communities or through nosocomial transmission such as patient-to-HCW and HCW-to-HCW [ [1] , [2] , [3] ]. To differentiate between community-acquired infection from hospital-acquired infection in HCWs, traditional epidemiological study alone may be inadequate [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

“…When there are ongoing outbreaks of COVID-19, healthcare workers (HCWs) may acquire the disease from communities or through nosocomial transmission such as patient-to-HCW and HCW-to-HCW [ [1] , [2] , [3] ]. To differentiate between community-acquired infection from hospital-acquired infection in HCWs, traditional epidemiological study alone may be inadequate [ 2 ]. Few studies have applied phylogenomics to investigate whether COVID-19-infected HCWs have acquired the disease in hospital [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

“…A follow-up investigation to differentiate between hospital-acquired and community-acquired infection in these two HCWs was therefore important. Whole-genome sequencing (WGS) had been applied to study the genomic epidemiology of SARS-CoV-2 in hospitals with known outbreaks; infected patients/HCWs with epidemiological links and identical viral genomes would indicate that intra-hospital transmission had occurred [ [2] , [3] , [4] , [5] , [6] ]. Hong Kong is a densely populated city with >7.5 million residents.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Healthcare workers acquired COVID-19 disease from patients? An investigation by phylogenomics

Wong

Lee

Siu

et al. 2021

Journal of Hospital Infection

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The increasing number of coronavirus disease 2019 cases in the community has posed a significant epidemic pressure on healthcare settings. When healthcare workers (HCWs) acquire COVID-19, contact tracing and epidemiological investigation might not be adequate for determining the source of transmission. Here, we report a phylogenetic investigation involving two infected HCWs and nine patients to determine whether patient-to-HCW transmission had occurred in a hospital without a previous COVID-19 outbreak. This is the first study to apply phylogenomics to investigate suspected nosocomial transmission in a region with low prevalence of COVID-19. Our results do not support the occurrence of direct patient-to-HCW transmission.

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Nanopore sequencing technology and its applications

Zheng

Zhou

Ding

et al. 2023

MedComm

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Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third‐generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID‐19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus‐2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID‐19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID‐19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.

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Investigation of intra-hospital SARS-CoV-2 transmission using nanopore whole-genome sequencing

Cited by 30 publications

References 35 publications

From RNA World to SARS-CoV-2: The Edited Story of RNA Viral Evolution

From RNA World to SARS-CoV-2: The Edited Story of RNA Viral Evolution

Healthcare workers acquired COVID-19 disease from patients? An investigation by phylogenomics

Nanopore sequencing technology and its applications

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